Stella - Stella is a multi-platform Atari 2600 VCS emulator released under the GNU General Public License...
Z26 - Z26 is one of the best emulators for the Atari 2600.
jGameBase - jGameBase is a fully-featured retro-gaming emulator frontend and game database utility.
Javatari - Javatari is a multiplayer Atari 2600 emulator written in pure Java with no external libs.
ProSystem - The ProSystem Emulator is an Atari 7800 emulator for the PC and Windows OS.
Steem Engine - Steem is an open source Atari STE emulator for Windows and Linux.